The design of this inflatable object was commissioned by the US Department of Homeland Security to be used in response to terrorist attacks against subways. But perhaps it could also be used to prevent future subway floods like those that happened recently in New York City:

The plugs can be inflated in about three minutes. But once inflated, they are pressurized with either air or water.

I can see this working in a single end-to-end tunnel, but subways are vast networks of tunnels with hundreds of access points - passenger entrances, ventilation shafts, maintenance ducts, etc. Failing to plug any one of them would allow water to enter the system. If there's a way in, water will find it.